Phoenix Sun
by Sinful Existence
Summary: The Patriots AI was shattered, but it had gathered far more information than anyone could have possibly foreseen. How far did their knowledge reach? How many contingency plans were in place? Rated M for general MGS violence and language.


This prologue pretty much turned out the way I planned, but the result is that it sounds very bad at first. I beg that people bear with me at least until chapter one is complete and you can see how things tie in. I'll just say that, despite how much this chapter may seem to hint at it, the main character is NOT an OC. Just trust me.

Full Summary: The Patriots AI was shattered, but it had gathered far more information than anyone could have possibly foreseen. How far did their knowledge reach? How many contingency plans were in place? And what would it take for them to rid themselves of the Patriots once and for all? How do you take out the Patriots when the world's greatest hero is dead?

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Prologue: Phoenix Sun  
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It wasn't that Dr. Jean Reedman liked working for the Patriots. Quite the contrary, she found their orders confusing and immoral. But it was by following those orders that she had all the research funding she could ask for, food on her table, and job security for the rest of her foreseeable life.

She had been working remotely with the team in Shadow Moses that had been working on REX. Granted, engineering was not her strong suit, but she had expertise in both humans and animals. They had been trying to figure out how to make a battle tank that could launch a nuke. It was obvious they couldn't just throw wheels on a chassis, stick a rail gun on it, and call it complete. The lead engineer, Dr. Hal Emmerich, suggested a bi-pedal dinosaur shape. They'd all laughed at first but oddly found that the shape he suggested worked both as a way to make sure the tank would be able to scale obstacles normal tanks couldn't drive around, as well as a way to stabilize the tank while firing the rail gun.

Obviously Reedman didn't have dinosaurs running around her lab, but she knew about the anatomy of similarly-shaped animals, to the point where she was necessary to make sure REX had proper handling and balance in motion.

The project had ended in failure, though. REX was complete, but it was immediately hijacked and used in a high-stakes gamble for the remains of Big Boss. She hadn't been on the team responsible for Les Enfants Terribles, however the lab she was in was the same lab. The current team descended from that which created the clones of Big Boss, thus she knew quite a bit about what was going on.

It was a shock to her when two years after the Shadow Moses Incident, she was contacted by her employers. Their orders were simple but ludicrous: create more clones of Big Boss. Not one, not two, but six. What did the Patriots want, a damn army? As usual, though, it wasn't her place to question. It was another order that would result in a nice sum of money. Sometimes life came down to choices like that: your morals or your livelihood?

They'd had Big Boss's corpse and therefore all the genetic material they could possibly need to make more clones. The project was split up among her teammates.

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It was times like this that Jean questioned if her morals were really so easy to throw away for money. For the job. She'd never put nanomachines in such a young person before. The effects of nanomachines on children was a test in progress but results had been inconclusive so far. It was a dangerous risk to take but the Patriots' orders were absolute on the matter. It had to be done and it had to be done at this stage, before the child progressed too far.

Jean was the last of the scientists to inject her child. She had wrestled with the idea more than anyone else.

Five of the other scientists watched over the other children, having split them up so each only had to deal with one child at a time. The Patriots approved of them being kept separate anyway. Observations with Liquid and Solid Snake had shown a tendency between clones to feel a need to one-up each other. They didn't need rivalries or other such nonsense.

So Jean had been given a single clone to take care of. Regardless of it being her job, regardless of the fact that this life, technically, was created, it was still a child. A child that had been given birth to. A child who moved and played and learned. He was almost like a son to Jean at this point. She'd been there for his first steps. His first laugh. She'd raised and nurtured him.

And now she was going to inject him with highly dangerous, microscopic machines that would rampage through his bloodstream in unforeseeable ways. It was too much to bear. But the threats were that if she could not cooperate, the child would have to be 'scrapped'. Like a piece of garbage. It infuriated her, but she gave him the injection. He was three at the time.

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Jean watched over the lip of her book as she watched her six-year-old charge getting karate lessons. Yet another order from the Patriots. He needed to be well-versed in combat, but as he was still too young to put through serious combat training without it being completely life-threatening and immoral, karate was the first start for him.

She had yet to see any changes in him, other than the fact that the nanomachines would heal his wounds at an accelerated rate. This was a relief to her but also a worry. It was good that the nanomachines weren't interfering with his life a lot. It would help him get accustomed to them. At the same time... what was their purpose? Was there something they were there for that she didn't know, that could activate at any moment? What was the purpose if the nanomachines weren't actually doing anything for him other than existing?

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The next year was an odd one for everyone and, really, a very stressful one.

She'd been in the lab's gardens with her charge when the first 'attack' happened. She'd been watching as the boy tried to catch a butterfly, smiling and laughing with him. Her face locked up mid-expression as she felt an entirely new feeling. It was like there was a brief moment where her soul, her very essence, had left her. It came rushing back in the next second however and it was like it was replaced with a molten, burning soul. Something that was burning her from the inside, setting her on fire. All the moral atrocities she'd committed as a scientist came rushing to her mind and heart in a surge of remorse, self-hatred, and longing to die. Her mind cycled through all the things she'd done, all the things she didn't remember running away from but she realized she never came to terms with.

What were her nanomachines doing? Weren't they supposed to regulate emotional surges like this? Why was she being allowed to suffer so much? Why wouldn't someone kill her and put her out of her misery!

The child, whose nanomachines interfered with him so little that whatever was happening had no impact on him, rushed to her and pulled a knife from her fingers, looking scared at her reactions. When did she pull out her emergency knife? She hadn't even remembered making the decision to stab herself but apparently her body had been moving for her.

After a moment the burning surge within her lessened and her body started to assume control again. Whatever had sent her nanomachines offline had been temporary and control was being reasserted. She pulled herself to her feet, wiping the drool that had been pooling from her mouth. She realized idly that she had had some kind of seizure from whatever happened.

She hugged the scared child to try to comfort him, putting him to bed before consulting with the other scientists. Everyone had felt the disturbance. A few scientists weren't as lucky as her to have someone stop them and killed themselves on the spot. It was a sad day but a confusing one as well.

She didn't find out until later, when the Patriots decided the information fit under what they needed to know, that the Sons of the Patriots system had temporarily been shut down in that moment the attacks happened. It had caused everyone's regulating nanomachines to stop working. Plans were being made to stop the force behind it, but they predicted it would not be the only time the nanomachines and SoP came offline.

They were right. Several more attacks happened as Liquid Ocelot tested the system, tried to figure out how to work around it. She was only thankful that these attacks seemed to not affect the child. The only effect came from his worry for her when she would freak out.

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The last attack was the worst and a day Jean would always remember. Her contact to the Patriots had inexplicably been cut off. She could no longer get in contact with her employers. Whenever she tried, she'd get a horrible static.

She wondered if this was a sign of another attack but she felt fine and relaxed. At least until she heard him scream.

She spun to face her charge and saw with horror that he was clutching his head, curled up in a fetal position on the floor. Vaguely, she could hear the screams of the other children in the facility, but they weren't her concern. She ran to her charge and checked him over for injury. He was seizing and shaking uncontrollably on the floor, his mouth foaming and his eyes rolled back in his head. She panicked and wondered why now? Why were his nanomachines affecting him this way and why was she spared? What was happening to the children?

His body gave one last giant heave before going still. His heart was racing and his breathing quickened but he was no longer conscious.

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Ever since the day the Patriots AI was destroyed, the children had been in comas. Unable to wake up from whatever the nanomachines had put them through. What on earth had happened? Why couldn't they wake up?

Talk had been circulating about terminating them and starting over, but after seven years? It was absurd. Furthermore, these weren't pieces of hardware you could toss and replace on a whim. These were human children. Clones or not, they deserved a chance at life. Besides, what deadline was there now? What purpose? The Patriots had wanted these clones made, but now their employers no longer existed. The clones were just children now.

It still steamed her. AI... that's what they had been listening to. Advanced AIs. It was frustrating that they hadn't even been real people. Not for a long time now.

It wasn't until ten years had passed when something happened. The clones had escaped. At least, the other five had. Hers was still in the hospital wing, but she was sure that if the others had woken up, he would too. It was a terrible loss to have the other children missing but her mind was on one thing: her clone. Her child. Was he okay? Would he wake up? Would he remember her?

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After the chaos of what was now being called the Outer Haven Incident, the country had been in shambles. It had taken some time for things to get put back together. One of those things being the government.

President Howard Stephenson was the first U.S. President in a long time to be more than just a figurehead. A puppet of the Patriots. No, he was an equal part of the governing body. It gave him an odd sense of pride, as well as pity to his predecessors.

He was nearing the end of his second term but honestly had no regrets. Things had gotten a lot better once the SoP system was out of the way. As inconvenient as it was now in some ways, at least vital things like electricity and water were still functioning. They were getting on with their lives.

He gave a start as he heard his phone ring, frowning a bit and stopping his packing. He'd asked not to be disturbed. It was rather late and he wanted to finish some last-minute packing before bed.

The call was insistent and it seemed no one in the office was around to answer it, so he strode over and picked up the receiver, keeping his voice as pleasant as possible, "Hello?"

There was nothing but silence on the other end and then pain. Endless pain that seemed to be concentrated in a matter of seconds. He clutched his head and fell against his desk, panting as it felt like his head was going to explode.

After a moment the pain vanished and a voice on the other end chuckled, "I hope that little gift is enough to show you that I'm serious about what I say next."

Stephenson gasped and panted for air, unable to keep the fury from his voice, "How did you do that? I would have listened without the unnecessary pain."

The voice laughed again, "Not really. Think about it, Mr. President. Listen to my voice. If someone with my voice tried to tell you what I'm about to tell you, would you honestly believe them and not think it a prank?"

He was begrudged to admit the person was right. It sounded like some punk kid having fun. He probably wouldn't have listened to them, though he still felt it had been unnecessary to do what they did. He hadn't felt so much pain since ten years ago. The thought made his blood run cold, the question leaving his lips on its own, "And what is it you need to tell me? Who are you?"

He could hear a smile in the person's voice. Whoever it was didn't even seem to have a shred of remorse for hurting him. Most likely the kind of psychotic who might have even found his pain amusing, "My name is John Doe. And we are the Patriots."

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So there's the wee little prologue. I know it's rough around the edges but like I said, give me time to write up chapter one before you make judgments.


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